Sonnenfeld confirmed the development to The Hollywood Reporter Wednesday.
Few plot details are known regarding the upcoming science-fiction comedy, which is expected to open in 3D in May 2011, Empire Online said.
The previous two "MIB" movies -- released in 1997 and 2002 -- featured Smith and Jones as U.S. government agents dealing with space aliens who come to Earth.
'Maze Runner' brings in $11.3M Friday
Dakota Fanning says her mother is no stage mom